The biological knowledge discovery by PCCF measure and PCA-F projection.

In the process of biological knowledge discovery, PCA is commonly used to complement the clustering analysis, but PCA typically gives the poor visualizations for most gene expression data sets. Here, we propose a PCCF measure, and use PCA-F to display clusters of PCCF, where PCCF and PCA-F are modeled from the modified cumulative probabilities of genes. From the analysis of simulated and experimental data sets, we demonstrate that PCCF is more appropriate and reliable for analyzing gene expression data compared to other commonly used distances or similarity measures, and PCA-F is a good visualization technique for identifying clusters of PCCF, where we aim at such data sets that the expression values of genes are collected at different time points.

Kinetic properties of Streptomyces canarius L- Glutaminase and its anticancer efficiency

Abstract L-glutaminase was produced by Streptomyces canarius FR (KC460654) with an apparent molecular mass of 44 kDa. It has 17.9 purification fold with a final specific activity 132.2 U/mg proteins and 28% yield recovery. The purified L-glutaminase showed a maximal activity against L-glutamine when incubated at pH 8.0 at 40 °C for 30 min. It maintained its stability at wide range of pH from 5.0 11.0 and thermal stable up to 60 °C with Tm value 57.5 °C. It has high affinity and catalytic activity for L-glutamine (Km 0.129 mM, Vmax 2.02 U/mg/min), followed by L-asparagine and L-aspartic acid. In vivo, L-glutaminase showed no observed changes in liver; kidney functions; hematological parameters and slight effect on RBCs and level of platelets after 10 days of rabbit's injection. The anticancer activity of L-glutaminase was also tested against five types of human cancer cell lines using MTT assay in vitro. L-glutaminase has a significant efficiency against Hep-G2 cell (IC50, 6.8 μg/mL) and HeLa cells (IC50, 8.3 μg/mL), while the growth of MCF-7 cells was not affected. L-glutaminase has a moderate cytotoxic effect against HCT-116 cell (IC50, 64.7 μg/mL) and RAW 264.7 cell (IC50, 59.3 μg/mL).

Synaptosomal lactate dehydrogenase isoenzyme composition is shifted toward aerobic forms in primate brain evolution.

With the evolution of a relatively large brain size in haplorhine primates (i.e. tarsiers, monkeys, apes, and humans), there have been associated changes in the molecular machinery that delivers energy to the neocortex. Here we investigated variation in lactate dehydrogenase (LDH) expression and isoenzyme composition of the neocortex and striatum in primates using quantitative Western blotting and isoenzyme analysis of total homogenates and synaptosomal fractions. Analysis of isoform expression revealed that LDH in synaptosomal fractions from both forebrain regions shifted towards a predominance of the heart-type, aerobic isoform LDH-B among haplorhines as compared to strepsirrhines (i.e. lorises and lemurs), while in the total homogenate of the neocortex and striatum there was no significant difference in LDH isoenzyme composition between the primate suborders. The largest increase occurred in synapse-associated LDH-B expression in the neocortex, with an especially remarkable elevation in the ratio of LDH-B/LDH-A in humans. The phylogenetic variation in the ratio of LDH-B/LDH-A was correlated with species-typical brain mass but not the encephalization quotient. A significant LDH-B increase in the subneuronal fraction from haplorhine neocortex and striatum suggests a relatively higher rate of aerobic glycolysis that is linked to synaptosomal mitochondrial metabolism. Our results indicate that there is a differential composition of LDH isoenzymes and metabolism in synaptic terminals that evolved in primates to meet increased energy requirements in association with brain enlargement.

Identification of novel phosphorylation modification sites in human proteins that originated after the human-chimpanzee divergence.

MOTIVATION: Phosphorylation modifications of specific protein residues are involved in a wide range of biological processes such as modulation of intracellular signal networks. Here, we present the development and application of a bioinformatics procedure for systematic identification of human-specific phosphorylation sites in proteins that may have occurred after the human-chimpanzee divergence. RESULTS: We collected annotated human phosphorylation sites and compared each site to orthologous mammalian proteins across taxa including chimpanzee, orangutan, rhesus macaque, marmoset, mouse, dog, cow, elephant, opossum and platypus. We identified 37 human-specific gains of annotated phosphorylation sites in 35 proteins: 22 serines, 12 threonines and 3 tyrosines. The novel phosphorylation sites are situated in highly conserved segments of the protein. Proteins with novel phosphorylation sites are involved in crucial biological processes such as cell division (AURKB, CASC5, MKI67 and PDCD4) and chromatin remodeling (HIRA, HIRIP3, HIST1H1T, NAP1L4 and LRWD1). Modified phosphorylatable residues produce novel target sites for protein kinases such as cyclin-dependent kinases and casein kinases, possibly resulting in rewiring and fine-tuning of phosphorylation regulatory networks. The potential human-specific phosphorylation sites identified in this study are useful as candidates for functional analysis to identify novel phenotypes in humans. CONTACT: hahny@cau.ac.kr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Comparative evaluation of six extended-interval gentamicin dosing regimens in premature and full-term neonates.

PURPOSE: Six extended-interval gentamicin dosing regimens were comparatively evaluated in premature and full-term neonates. METHODS: Data regarding six physician-ordered dosing regimens of gentamicin for neonates in a hospital neonatal intensive care unit were collected and analyzed. Neonates of gestational age (GA) 29 weeks or younger received 4.5 mg/kg every 48 hours. Neonates of GA 30-34 weeks received one of three dosing regimens: 3.5, 4, or 4.5 mg/kg every 36 hours. Neonates of GA 35 weeks or older received either 3.5 or 4 mg/kg every 24 hours. Blood samples were collected 30 minutes before and 30 minutes after the third dose was infused for binary trough and peak level determinations, respectively. RESULTS: Peak gentamicin concentrations in the target range were attained most often in neonates of GA 29 weeks or younger who received gentamicin 4.5 mg/kg every 48 hours, in neonates of GA 30-34 weeks treated with gentamicin 3.5 mg/kg every 36 hours, and in neonates of GA 35 weeks or older treated with gentamicin 3.5 mg/kg every 24 hours. CONCLUSION: For neonates of GA 30-34 weeks, gentamicin 3.5 mg/kg every 36 hours resulted in the highest percentage of peaks in the target range compared with 4 and 4.5 mg/kg every 36 hours. For neonates of GA 35 weeks or older, gentamicin 3.5 mg/kg every 24 hours provided the highest percentage of peaks in the target range compared with 4 mg/kg every 24 hours. The differences between the percentages of trough values in the target range of 0.5-2 µg/mL were not significant among dosing subgroups within each age group.

Protein abundances are more conserved than mRNA abundances across diverse taxa.

Proteins play major roles in most biological processes; as a consequence, protein expression levels are highly regulated. While extensive post-transcriptional, translational and protein degradation control clearly influence protein concentration and functionality, it is often thought that protein abundances are primarily determined by the abundances of the corresponding mRNAs. Hence surprisingly, a recent study showed that abundances of orthologous nematode and fly proteins correlate better than their corresponding mRNA abundances. We tested if this phenomenon is general by collecting and testing matching large-scale protein and mRNA expression data sets from seven different species: two bacteria, yeast, nematode, fly, human, and rice. We find that steady-state abundances of proteins show significantly higher correlation across these diverse phylogenetic taxa than the abundances of their corresponding mRNAs (p=0.0008, paired Wilcoxon). These data support the presence of strong selective pressure to maintain protein abundances during evolution, even when mRNA abundances diverge.

Helicobacter pylori heat shock protein 60 antibodies are associated with gastric cancer.

Helicobacter pylori infection causes atrophic gastritis, peptic ulcer, and gastric cancer. The host immune response plays an important role in the pathogenesis of H. pylori-related diseases. Heat shock proteins are antigens involved in various diseases. This study evaluated seropositivity for antibodies to H. pylori heat shock protein 60 in patients with gastric cancer. Serum samples were obtained from 57 patients with gastric cancer (25 patients with diffuse-type gastric cancer and 32 with intestinal-type gastric cancer), 45 H. pylori-positive patients, and 49 H. pylori-negative patients without gastric cancer. Antibodies to heat shock protein 60 and H. pylori were assessed by enzyme-linked immunosorbent assay. The positivity rate for antibodies to hsp60 was significantly higher in H. pylori-positive patients than in H. pylori-negative patients (73.3% vs. 24.5%, p<0.001). In addition, the positivity rate for antibodies to hsp60 was higher in patients with gastric cancer than in H. pylori-positive patients without gastric cancer (87.7% vs. 73.3%, p=0.06), and the positivity rate for antibodies to hsp60 was significantly higher in patients with diffuse-type gastric cancer than in H. pylori-positive patients without gastric cancer (96% vs. 73.3%, p<0.05). H. pylori hsp60 might be associated with gastric carcinogenesis, especially in the case of diffuse cancer.

Toxicity of sucralose in humans: a review / Toxicidad de la sucralosa en humanos: una revisión

Sucralose is a non-nutritive artificial sweetener, 600 times sweeter than sucrose, and is very stable at high temperatures, among other characteristics. It was approved by the FDA, in 1999, to be utilized in foods, beverages, pharmaceutical products, diets and vitamin supplements. Studies suggest a diffusion, through the placental barrier, of small doses of sucralose and its metabolites. Its hydrolysis products (4-CG e 1,6-DCF) are more rapidly absorbed than sucralose: 4-CG is excreted intact in the urine, and 1,6-DCF undergoes reduction with elimination by the urine or rapid conjugation with glutathione. Various organs can be affected by ingestión of high doses of sucralose. As a result of the rise in global consumption of sweeteners and light- or diet-type products, studies are necessary to evaluate the action of this substance in the human species. The present study aims to accomplish a review of the literature that involves its indications of use, pharmacodynamics as well as the carcinogenic, teratogenic, neurotoxic, and nephrotoxic potentials of sucralose.

La sucralosa es un edulcorante artificial no nutritivo, 600 veces más dulce que la sacarosa, y es muy estable a altas temperaturas, entre otras características. Fue aprobado por la FDA, en 1999, para ser utilizada en los alimentos, bebidas, productos farmacéuticos, dietéticos y suplementos vitamínicos. Los estudios sugieren una difusión a través de la barrera placentaria, de pequeñas dosis de la sucralosa y sus metabolitos. Sus productos de hidrólisis (4-CG e 1,6-DCF) se absorben más rápidamente que la sucralosa: 4-CG se excreta intacta en la orina, y el 1,6-DCF sufre reducción con la eliminación por la orina o la rápida conjugación con glutatión. Diversos órganos pueden verse afectados por la ingestión de altas dosis de sucralosa. Como resultado del aumento en el consumo mundial de los edulcorantes y productos de tipo light o diet, son necesarias investigaciones para evaluar la acción de esta sustancia en la especie humana. El presente estudio tiene como objetivo realizar una revisión de la literatura que trata de las indicaciones de uso, la farmacodinamia, así como los potencialidades cancerígenas, teratogénicas, neurotóxicas y nefrotóxicas de la sucralosa.

Global reconstruction of the human metabolic network based on genomic and bibliomic data.

Metabolism is a vital cellular process, and its malfunction is a major contributor to human disease. Metabolic networks are complex and highly interconnected, and thus systems-level computational approaches are required to elucidate and understand metabolic genotype-phenotype relationships. We have manually reconstructed the global human metabolic network based on Build 35 of the genome annotation and a comprehensive evaluation of >50 years of legacy data (i.e., bibliomic data). Herein we describe the reconstruction process and demonstrate how the resulting genome-scale (or global) network can be used (i) for the discovery of missing information, (ii) for the formulation of an in silico model, and (iii) as a structured context for analyzing high-throughput biological data sets. Our comprehensive evaluation of the literature revealed many gaps in the current understanding of human metabolism that require future experimental investigation. Mathematical analysis of network structure elucidated the implications of intracellular compartmentalization and the potential use of correlated reaction sets for alternative drug target identification. Integrated analysis of high-throughput data sets within the context of the reconstruction enabled a global assessment of functional metabolic states. These results highlight some of the applications enabled by the reconstructed human metabolic network. The establishment of this network represents an important step toward genome-scale human systems biology.

Cholera toxin indirectly activates human monocyte-derived dendritic cells in vitro through the production of soluble factors, including prostaglandin E(2) and nitric oxide.

Cholera toxin (CT) is a potent adjuvant that activates dendritic cells (DC) by increasing intracellular cyclic AMP (cAMP) levels. In vivo and in vitro, very small amounts of CT induce potent adjuvant effects and activate DC. We hypothesized that DC intoxicated by CT may release factors that enhance their own maturation and induce the maturation of toxin-free bystander DC. Through the use of mixed cultures and transwell cultures, we found that human monocyte-derived DC (MDDC) pulsed with CT or other cAMP-elevating agonists induce the maturation of bystander DC. Many DC agonists including CT increase the production of prostaglandin E(2) (PGE(2)) and nitric oxide (NO). For this reason, we determined whether the actions of PGE(2) or NO are involved in the maturation of MDDC induced by CT or dibutyryl-cAMP (d-cAMP). We found that blocking the production of PGE(2) or blocking prostaglandin receptors inhibited MDDC maturation induced by CT and d-cAMP. Likewise, sequestering NO or blocking the downstream actions of NO resulted in the inhibition of MDDC maturation induced by CT and d-cAMP. These results indicate that endogenously produced factors including PGE(2) and NO contribute to the maturation of DC induced by CT and that these factors participate in bystander DC maturation. The results of this study may help explain why bacterial toxins that elevate cAMP are such potent adjuvants.

Hsp72 recognizes a P binding motif in the measles virus N protein C-terminus.

The major inducible 70-kDa heat shock protein (hsp72) binds measles virus (MV) nucleocapsids and increases MV gene expression. The cytoplasmic tail of the MV N protein (N(TAIL)) contains three hydrophobic domains (Box-1-3) that are potential targets of hsp72 interaction. Low affinity binding to Box-3 is correlated to hsp72-dependent stimulation of MV minireplicon reporter gene expression whereas interactions between hsp72 and Box-1 and/or -2 have not been documented. The present work showed that virus deficient in Box-3/hsp72 interaction retains the ability to form nucleocapsid/hsp72 complexes, identifying Box-2 but not Box-1 as a mediator of high affinity hsp72 binding. Box-2 is the binding site for the viral P protein X domain (XD), where P tethers the viral polymerase to nucleocapsid in support of transcription and genome replication, and competitive inhibition of XD binding to N(TAIL) by hsp72 was shown. Recognition of a common binding site by P and hsp72 represents a potential mechanism for host cell modulation of viral gene expression.